Package: methylCC 1.19.0

Stephanie C. Hicks

methylCC: Estimate the cell composition of whole blood in DNA methylation samples

A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

Authors:Stephanie C. Hicks [aut, cre], Rafael Irizarry [aut]

methylCC_1.19.0.tar.gz
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methylCC.pdf |methylCC.html✨
methylCC/json (API)
NEWS

# Install 'methylCC' in R:

install.packages('methylCC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stephaniehicks/methylcc/issues

Datasets:

FlowSorted.Blood.450k.sub - A reduced size of the FlowSorted.Blood.450k dataset
offMethRegions - Unmethylated regions for all celltypes
onMethRegions - Methylated regions for all celltypes

On BioConductor:methylCC-1.19.0(bioc 3.20)methylCC-1.18.0(bioc 3.19)

bioconductor-package

2 exports 1.24 score 145 dependencies 2 mentions

Last updated 2 months agofrom:9e2f073390

Exports:cell_counts estimatecc

Dependencies:abind annotate AnnotationDbi askpass base64 beachmat beanplot BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bsseq bumphunter cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi farver fastmap FlowSorted.Blood.450k foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue gtools HDF5Array hms httr IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest illuminaio IRanges iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest munsell nlme nor1mix openssl permute pillar pkgconfig plogr plyr plyranges png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales scrime siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract raw data	.extract_raw_data
Finding differentially methylated regions	.find_dmrs
.initialize_theta	.initialize_theta
.initializeMLEs	.initializeMLEs
.methylcc_engine	.methylcc_engine
Expectation step	.methylcc_estep
Maximization step	.methylcc_mstep
Pick target positions	.pick_target_positions
.preprocess_estimatecc	.preprocess_estimatecc
.splitit	.splitit
Helper function to take the product of Z and cell composition estimates	.WFun
Generic function that returns the cell composition estimates	cell_counts cell_counts,estimatecc-method
Estimate cell composition from DNAm data	estimatecc
the estimatecc class	estimatecc-class
A reduced size of the FlowSorted.Blood.450k dataset	FlowSorted.Blood.450k.sub
Unmethylated regions for all celltypes	offMethRegions
Methylated regions for all celltypes	onMethRegions

Usage by other packages (reverse dependencies)